def getVariants(self, referenceName, startPosition, endPosition,
variantName=None, callSetIds=None):
"""
Returns an iterator over the specified variants. The parameters
correspond to the attributes of a GASearchVariantsRequest object.
"""
if variantName is not None:
raise exceptions.NotImplementedException(
"Searching by variantName is not supported")
# For v0.5.1, callSetIds=[] actually means return all callSets.
# In v0.6+, callSetIds=[] means return no call sets, and
# callSetIds=None means return all call sets. For forward
# compatibility, we use the 0.6 interface for this function but
# we translate back to the 0.5 interface while we support this.
# TODO Remove this comment and workaround once we transition to
# protocol version 0.6
if callSetIds is None:
callSetIds = []
else:
for callSetId in callSetIds:
if callSetId not in self._callSetIds:
raise exceptions.CallSetNotInVariantSetException(
callSetId, self.getId())
if len(callSetIds) == 0:
callSetIds = self._callSetIds
if referenceName in self._chromFileMap:
varFileName = self._chromFileMap[referenceName]
referenceName, startPosition, endPosition = \
self.sanitizeVariantFileFetch(
referenceName, startPosition, endPosition)
cursor = self.getFileHandle(varFileName).fetch(
referenceName, startPosition, endPosition)
for record in cursor:
yield self.convertVariant(record, callSetIds)
def _getDatasetFromReadsRequest(self, request):
if len(request.readGroupIds) != 1:
raise exceptions.NotImplementedException(
"Exactly one read group id must be specified")
compoundId = request.readGroupIds[0]
dataset = self._getDatasetFromCompoundId(compoundId)
return dataset
def testNotImplementedException(self):
message = "A string unlikely to occur at random."
exception = exceptions.NotImplementedException(message)
response = frontend.handleException(exception)
self.assertEquals(response.status_code, 501)
gaException = self.getGa4ghException(response.data)
self.assertEquals(gaException.message, message)
def _getDatasetFromVariantsRequest(self, request):
variantSetIds = request.variantSetIds
if len(variantSetIds) != 1:
raise exceptions.NotImplementedException(
"Exactly one variant set id must be specified")
compoundId = request.variantSetIds[0]
dataset = self._getDatasetFromCompoundId(compoundId)
return dataset
def oidcCallback():
"""
Once the authorization provider has cleared the user, the browser
is returned here with a code. This function takes that code and
checks it with the authorization provider to prove that it is valid,
and get a bit more information about the user (which we don't use).
A token is generated and given to the user, and the authorization info
retrieved above is stored against this token. Later, when a client
connects with this token, it is assumed to be a valid user.
:return: A display of the authentication token to use in the client. If
OIDC is not configured, raises a NotImplementedException.
"""
if app.oidcClient is None:
raise exceptions.NotImplementedException()
response = dict(flask.request.args.iteritems(multi=True))
aresp = app.oidcClient.parse_response(
message.AuthorizationResponse,
info=response,
sformat='dict')
sessState = flask.session.get('state')
respState = aresp['state']
if (not isinstance(aresp, message.AuthorizationResponse) or
respState != sessState):
raise exceptions.NotAuthenticatedException()
args = {
"code": aresp['code'],
"redirect_uri": app.oidcClient.redirect_uris[0],
"client_id": app.oidcClient.client_id,
"client_secret": app.oidcClient.client_secret
}
atr = app.oidcClient.do_access_token_request(
scope="openid",
state=respState,
request_args=args)
if not isinstance(atr, message.AccessTokenResponse):
raise exceptions.NotAuthenticatedException()
atrDict = atr.to_dict()
if flask.session.get('nonce') != atrDict['id_token']['nonce']:
raise exceptions.NotAuthenticatedException()
key = oic.oauth2.rndstr(SECRET_KEY_LENGTH)
flask.session['key'] = key
app.tokenMap[key] = aresp["code"], respState, atrDict
# flask.url_for is broken. It relies on SERVER_NAME for both name
# and port, and defaults to 'localhost' if not found. Therefore
# we need to fix the returned url
indexUrl = flask.url_for('index', _external=True)
indexParts = list(urlparse.urlparse(indexUrl))
if ':' not in indexParts[1]:
indexParts[1] = '{}:{}'.format(socket.gethostname(), app.myPort)
indexUrl = urlparse.urlunparse(indexParts)
response = flask.redirect(indexUrl)
return response
def _getContainer(self):
if len(self._request.readGroupIds) != 1:
if len(self._request.readGroupIds) == 0:
msg = "Read search requires a readGroup to be specified"
else:
msg = "Read search over multiple readGroups not supported"
raise exceptions.NotImplementedException(msg)
readGroupId = self._request.readGroupIds[0]
readGroup = _safeMapQuery(self._containerIdMap, readGroupId,
exceptions.ReadGroupNotFoundException)
return readGroup
def _getPrefix(self, url):
"""
Given a url return namespace prefix.
Leverages prefixes already in graph namespace
Ex. "http://www.drugbank.ca/drugs/" -> "Drugbank"
"""
for prefix, namespace in self._rdfGraph.namespaces():
if namespace.toPython() == url or namespace == url:
return prefix
raise exceptions.NotImplementedException(
"No namespace found for url {}".format(url))
def callSetsGenerator(self, request):
"""
Returns a generator over the (callSet, nextPageToken) pairs defined
by the specified request.
"""
if request.name is not None:
raise exceptions.NotImplementedException(
"Searching over names is not supported")
variantSet = _getVariantSet(request, self._variantSetIdMap)
return self._topLevelObjectGenerator(
request, variantSet.getCallSetIdMap(),
variantSet.getCallSetIds())
def _toNamespaceURL(self, term):
"""
Given an ontologyterm.term return namespace identifier.
Leverages prefixes already in graph namespace
Ex. "DrugBank:DB01268" -> "http://www.drugbank.ca/drugs/DB01268"
"""
termPrefix, termId = term.split(':')
for prefix, namespace in self._rdfGraph.namespaces():
if prefix == termPrefix:
return "".join([namespace, termId])
raise exceptions.NotImplementedException(
"Term has a prefix not found in this instance. {}".format(term))
def _getContainer(self):
if len(self._request.readGroupIds) != 1:
if len(self._request.readGroupIds) == 0:
msg = "Read search requires a readGroup to be specified"
else:
msg = "Read search over multiple readGroups not supported"
raise exceptions.NotImplementedException(msg)
readGroupId = self._request.readGroupIds[0]
try:
readGroup = self._containerIdMap[self._request.readGroupIds[0]]
except KeyError:
raise exceptions.ReadGroupNotFoundException(readGroupId)
return readGroup
def _getVariantSet(request, variantSetIdMap):
if len(request.variantSetIds) != 1:
if len(request.variantSetIds) == 0:
msg = "Variant search requires specifying a variantSet"
else:
msg = ("Variant search over multiple variantSets "
"not supported")
raise exceptions.NotImplementedException(msg)
variantSetId = request.variantSetIds[0]
try:
variantSet = variantSetIdMap[variantSetId]
except KeyError:
raise exceptions.VariantSetNotFoundException(variantSetId)
return variantSet
def callSetsGenerator(self, request):
"""
Returns a generator over the (callSet, nextPageToken) pairs defined
by the specified request.
"""
if request.name is not None:
raise exceptions.NotImplementedException(
"Searching over names is not supported")
compoundId = datamodel.VariantSetCompoundId.parse(request.variantSetId)
dataset = self.getDataset(compoundId.datasetId)
variantSet = _getVariantSet(request, dataset.getVariantSetIdMap())
return self._topLevelObjectGenerator(request,
variantSet.getCallSetIdMap(),
variantSet.getCallSetIds())
def readsGenerator(self, request):
"""
Returns a generator over the (read, nextPageToken) pairs defined
by the specified request
"""
if request.referenceId is None:
raise exceptions.UnmappedReadsNotSupported()
if len(request.readGroupIds) != 1:
raise exceptions.NotImplementedException(
"Exactly one read group id must be specified")
compoundId = datamodel.ReadGroupCompoundId.parse(
request.readGroupIds[0])
dataset = self.getDataset(compoundId.datasetId)
intervalIterator = ReadsIntervalIterator(request,
dataset.getReadGroupIdMap())
return intervalIterator
def getAllele(version, id):
raise exceptions.NotImplementedException()
def getVariantSetSequence(version, vsid, sid):
raise exceptions.NotImplementedException()
def getSequenceBases(version, id):
raise exceptions.NotImplementedException()
def getMode(version, mode):
raise exceptions.NotImplementedException()
def searchJoins(version):
raise exceptions.NotImplementedException()
def getVariant(version, id):
raise exceptions.NotImplementedException()
def searchSequences(version):
raise exceptions.NotImplementedException()
def searchIndividualGroups(version):
raise exceptions.NotImplementedException()
def searchExperiments(version):
raise exceptions.NotImplementedException()
def searchGenotypePephenotype(version):
raise exceptions.NotImplementedException()
def getReadGroup(version, id):
raise exceptions.NotImplementedException()
def getDataset(version, id):
raise exceptions.NotImplementedException()
def searchFeatures(version):
raise exceptions.NotImplementedException()
def searchVariantSetSequences(version, id):
raise exceptions.NotImplementedException()
def searchAlleles(version):
raise exceptions.NotImplementedException()
def subgraphJoins(version):
raise exceptions.NotImplementedException()
def getFeature(version, id):
raise exceptions.NotImplementedException()